I don't believe that the Pokémon franchise will ever create a everlasting story or a story to remember. In the end it all comes down to beating the Elite Four and becoming the Champion. I don't mean that the stories in the games are useless or doesn't hold any meaning behind it, but it just doesn't hit me due the overall shortage of the game, I believe the main games of Pokémon are not capable of greating a memorable story because the gameplay's time are/is to short - If they make a spin-off series with a day-by-day feature (Such feature what the Persona games possess) then the story and plot would be of the essence.

A little off topic here, now I think about it a Pokémon game in Persona's style wouldn't be that bad of a idea overall.